Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCORL1

Cell type

Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous

Attributes by original data submitter

Sample

source_name
K562 cell line
genotype
BCORKO
chip antibody
BCORL1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For histone ChIP-seq analysis, cells were cross-linked for 10 min with 1% formaldehyde at room temperature on a shaker at 850rpm. Crosslinked nuclei were quenched with 0.125 M glycine for 5 minutes at room temperature and washed with PBS (containing protease inhibitor and HDAC inhibitor Sodium Butyrate (NaBut)). For ChIP-seq analysis of BCOR, BCORL1, RNF2, KDM2B, and SUZ12, cells were first fixed with 2 mM DSG for 45 min at RT, followed by formaldehyde cross-linking as described above. After fixation, pellets were resuspended in 500 ul of 1% SDS (50 mM Tris-HCl pH 8, 10 mM EDTA) and sonicated in 1 ml AFA fiber millitubes for 25 minutes using a Covaris E220 instrument (setting: 75 peak incident power, 5% duty factor and 200 cycles per burst). Chromatin was immunoprecipitated using primary antibody and Dynabeads® Protein A/G. ChIP-seq libraries were made using the ThruPLEX DNA-seq 48D Rubicon kit and purified. 75-bp single-end reads were sequenced on an Illumina NextSeq instrument.

Sequencing Platform

instrument_model
NextSeq 550

hg38

Number of total reads
29589734
Reads aligned (%)
68.9
Duplicates removed (%)
27.9
Number of peaks
22438 (qval < 1E-05)

hg19

Number of total reads
29589734
Reads aligned (%)
68.4
Duplicates removed (%)
29.2
Number of peaks
22228 (qval < 1E-05)

Base call quality data from DBCLS SRA